Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 234 bits (596), Expect = 3e-66 Identities = 127/281 (45%), Positives = 175/281 (62%), Gaps = 10/281 (3%) Query: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 +++ + K +G+ + +INL I G+ V +GPSGCGK+T+LR +AGLE S G+I I Sbjct: 7 VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66 Query: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123 G DVT RD+ MVFQSYAL+PHM++ EN+ +G+K+ G K R+ EA ++ L Sbjct: 67 GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDL 126 Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183 E + DR Q+SGGQ+QRVA+ RA++ P V LFDEPLSNLDA LR MR ++ L KQ Sbjct: 127 EGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQF 186 Query: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFS 243 T +YVTHDQ EA ++D ++V+N+G I Q+GSP DLY +P SRF+A F+G + + Sbjct: 187 DITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDANLFPAT 246 Query: 244 SDVGLQDI---SLDASAAF-------VGCRPEHIEIVPDGD 274 G DI L F VG RPE I + G+ Sbjct: 247 FSDGYVDIYGYHLPRPLHFGTQGEGMVGVRPEAITLSDRGE 287 Lambda K H 0.320 0.139 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 294 Number of extensions: 10 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 348 Length adjustment: 29 Effective length of query: 309 Effective length of database: 319 Effective search space: 98571 Effective search space used: 98571 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory